Proteins

A representation of the 3D structure of myoglobin,
showing coloured alpha helices. This protein was the first to
have its structure solved by X-ray crystallography by Max Perutz
and Sir John Cowdery Kendrew in 1958, which led to them receiving
a Nobel Prize in Chemistry.

A protein is a complex, high-molecular-weight organic compound that
consists of amino acids joined by peptide bonds. Proteins are essential
to the structure and function of all living cells and viruses. Many
proteins are enzymes or subunits of enzymes. Other proteins play structural
or mechanical roles, such as those that form the struts and joints of
the cytoskeleton, serving as biological scaffolds for the mechanical
integrity and tissue signalling functions. Still more functions filled
by proteins include immune response and the storage and transport of
various ligands. In nutrition, proteins serve as the source of amino
acids for organisms that do not synthesize those amino acids natively.

Proteins are one of the classes of bio-macromolecules, alongside polysaccharides,
lipids, and nucleic acids, that make up the primary constituents of
living things. They are among the most actively-studied molecules in
biochemistry, and were discovered by Jöns Jakob Berzelius in 1838.

Almost all natural proteins are encoded by DNA. DNA is transcribed
to yield RNA, which serves as a template for translation by ribosomes.

Properties of Proteins

Proteins are amino acid chains that fold into unique 3-dimensional
structures. The shape into which a protein naturally folds is known
as its native state, which is determined by its sequence of amino acids.
Biochemists refer to four distinct aspects of a protein's structure:

* Primary structure: the amino acid sequence
* Secondary structure: highly patterned sub-structures—alpha helix
and beta sheet—or segments of chain that assume no stable shape.
Secondary structures are locally defined, meaning that there can be
many different secondary motifs present in one single protein molecule.
* Tertiary structure: the overall shape of a single protein molecule;
the spatial relationship of the secondary structural motifs to one another
* Quaternary structure: the shape or structure that results from the
union of more than one protein molecule, usually called subunit proteins
subunits in this context, which function as part of the larger assembly
or protein complex.

In addition to these levels of structure, proteins may shift between
several similar structures in performing their biological function.
In the context of these functional rearrangements, these tertiary or
quaternary structures are usually referred to as "conformations,"
and transitions between them are called conformational changes.

Proteins are separated into two groups: Complete and Incomplete. Incomplete
proteins are from plants and do not include all 20 amino acids. Complete
proteins come from an animal and include all 20 amino acids. You get
protein from mostly everything you eat, but whether all the amino acids
are in them depends on what the substance is.

The primary structure is held together by covalent peptide bonds, which
are made during the process of translation. The secondary structures
are held together by hydrogen bonds. The tertiary structure is held
together primarily by hydrophobic interactions but hydrogen bonds, ionic
interactions, and disulfide bonds are usually involved too.

The process by which the higher structures form is called protein folding
and is a consequence of the primary structure. The mechanism of protein
folding is not entirely understood. Although any unique polypeptide
may have more than one stable folded conformation, each conformation
has its own biological activity and only one conformation is considered
to be the active, or native conformation.

The two ends of the amino acid chain are referred to as the carboxy
terminus (C-terminus) and the amino terminus (N-terminus) based on the
nature of the free group on each extremity.

Working with proteins

Proteins are sensitive to their environment. They may only be active
in their native state, over a small pH range, and under solution conditions
with a minimum quantity of electrolytes. A protein in its native state
is often described as folded. A protein that is not in its native state
is said to be denatured. Denatured proteins generally have no well-defined
secondary structure. Many proteins denature and will not remain in solution
in distilled water.

One of the more striking discoveries of the 20th century was that the
native and denatured states in many proteins were interconvertible,
that by careful control of solution conditions (by for example, dialyzing
away a denaturing chemical), a denatured protein could be converted
to native form. The issue of how proteins arrive at their native state
is an important area of biochemical study, called the study of protein
folding.

Through genetic engineering, researchers can alter the sequence and
hence the structure, "targeting", susceptibility to regulation
and other properties of a protein. The genetic sequences of different
proteins may be spliced together to create "chimeric" proteins
that possess properties of both. This form of tinkering represents one
of the chief tools of cell and molecular biologists to change and to
probe the workings of cells. Another area of protein research attempts
to engineer proteins with entirely new properties or functions, a field
known as protein engineering.

Protein-protein interactions can be screened for using two-hybrid screening.

Protein regulation

Various molecules and ions are able to bind to specific sites on proteins.
These sites are called binding sites. They exhibit chemical specificity.
The particle that binds is called a ligand. The strength of ligand-protein
binding is a property of the binding site known as affinity.

Since proteins are involved in practically every function performed
by a cell, the mechanisms for controlling these functions therefore
depend on controlling protein activity. Regulation can involve a protein's
shape or concentration. Some forms of regulation include:

* Allosteric modulation: When the binding of a ligand at one site
on a protein affects the binding of ligand at another site.
* Covalent modulation: When the covalent modification of a protein affects
the binding of a ligand or some other aspect of the protein's function.

Diversity

Proteins are generally large molecules, having molecular masses of
up to 3,000,000 (the muscle protein titin has a single amino acid chain
27,000 subunits long). Such long chains of amino acids are almost universally
referred to as proteins, but shorter strings of amino acids are referred
to as "polypeptides," "peptides" or rarely, "oligopeptides".
The dividing line is undefined, though "polypeptide" usually
refers to an amino acid chain lacking tertiary structure which may be
more likely to act as a hormone (like insulin), rather than as an enzyme
(which depends on its defined tertiary structure for functionality).

Proteins are generally classified as soluble, filamentous or membrane-associated
(see integral membrane protein). Nearly all the biological catalysts
known as enzymes are soluble proteins (with a recent notable execption
being the discovery of ribozymes, RNA molecules with the catalytic properties
of enzymes.) Antibodies, the basis of the adaptive immune system, are
another example of soluble proteins. Membrane-associated proteins include
exchangers and ion channels, which move their substrates from place
to place but do not change them; receptors, which do not modify their
substrates but may simply shift shape upon binding them. Filamentous
proteins make up the cytoskeleton of cells and much of the structure
of animals: examples include tubulin, actin, collagen and keratin, all
of which are important components of skin, hair, and cartilage. Another
special class of proteins consists of motor proteins such as myosin,
kinesin, and dynein. These proteins are "molecular motors,"
generating physical force which can move organelles, cells, and entire
muscles.

Role of Protein

Functions

Proteins are involved in practically every function performed by a
cell, including regulation of cellular functions such as signal transduction
and metabolism. For example, protein catabolism requires enzymes termed
proteases and other enzymes such as glycosidases.

Within Nutrition

Protein is an important macronutrient to the human diet, supplying
the body's needs for nitrogen and amino acids, the building blocks of
proteins. The exact amount of dietary protein needed to satisfy these
requirements may vary widely depending on age, sex, level of physical
activity, and medical condition, as well as the RDA specified by the
state.

The reccomended intake of protein differs from country to country,
but it is marginalised between 0.8 and 1.2g / kg b.w (Per kilogram of
bodyweight), however , in more serious athletes, requiring strength,
the figure is somewhat between 1.0 and 2.0g per kilogram of Body weight,
which is referred to as the maximum protein intake:benefits ratio. Although
Proteins are found in all foods, be it only in small amounts, protein
is still well concentrated in foods such as legumes, nuts, meat, and
dairy products the majority of which are protein choices for vegetarians.

Protein is the major component in the regulation, growth and differentation
of muscles, tendons, enzymes, skin, hair, eyes, as well as a tremendous
variety of other organs and processes. The quality of protein intake
is particularly important because different proteins supply essential
amino acids in different proportions. Given an adequate intake of nitrogen,
the human body can manufacture 10 of the 18 amino acids from glucose.
The remaining 8 amino acids (threonine, valine, tryptophan, isoleucine,
leucine, lysine, phenylalanine, and methionine) cannot be manufactured
by the body and must be acquired through supplementation. Thus, they
are termed essential amino acids.

For use within the body, the majority of protein taken from food consumed
is converted by protein catabolism into ammonia which, due to its toxicity,
must be converted to either urea or uric acid,or in some animals is
excreted in urine. Proteins possessing equal proportions of all essential
amino acids in relatively abundant quantities are often termed "complete",
or "High-Quality" Proteins, which are generally obtained from
Animal Proteins, such as meat, and are rated using PDCAAS (Protein Digestibility
Corrected Amino Acid Score).

Despite what the name suggests, quality proteins are not essential
for good supplementation or nutrition within the average person, however,
the difference between Amino Acids in Plant and Animal proteins is discernable,
particularly for athletes or bodybuilders as Plant Proteins lack two
major Amino acids found in Animal proteins ; Lysine within Grains, and
Methionine within Legumes, major benefactors to a major athlete's dietary
regime. Neverthelss, in terms of quality, amino acids found in Plant
and Animal extracts are identical.

Protein deficiency can lead to symptoms such as fatigue, insulin resistance,
hair loss, loss of hair pigment, loss of muscle mass , low body temperature,
hormonal irregularities, as well as loss of skin elsaticity. Severe
protein deficiency, encountered only in times of famine, is fatal, due
to the lack of material for the body to facilitate as energy.

It has been known that in some "wild diets", in which people
lose mass amounts of weight in a short period of time are attributed
to deficiencies in Protein, and thus loss in muscle mass, and not fat,
which is widely known as a dangerous practice, particularly because
of the benefits of Muscle mass over Fat.

Excessive protein intake has also been linked to several problems -

* overreaction within the immune system
* liver dysfunction due to increased toxic residues
* loss of bone density, frailty of bones due to increased acidity in
the blood and foundering (foot problems) in horses.

It is assumed by reasearchers on the field, that excessive intake of
protein forced increased calcium excretion. If there is to be excessive
intake of protein, it is thought that a regular intake of calcium would
be able to stablilise, or even increase the uptake of calcium by the
small intestine, which would be more beneficial in older women.

Proteins are often progenitors in allergies and allergic reactions
to certain foods. This is because the structure of each form of protein
is slightly different; some may trigger a response from the immune system
while others remain perfectly safe. Many people are allergic to casein,
the protein in milk; gluten, the protein in wheat and other grains;
the particular proteins found in peanuts; or those in shellfish or other
seafoods. It is extremely unusual for the same person to adversely react
to more than two different types of proteins, due to the diversity between
Protein or Amino Acid types.